MBB1 Topics Midterm PDF

I. CELL CHEMISTRY AND BIOENERGETICS Water Molecules Biochemistry (biological chemistry) is a Water is a polar molecule, with a slight field of science that deals with the structure, negative charge (δ-) on the oxygen atom and a f...

I. CELL CHEMISTRY AND BIOENERGETICS Water Molecules Biochemistry (biological chemistry) is a Water is a polar molecule, with a slight field of science that deals with the structure, negative charge (δ-) on the oxygen atom and a functions, and interactions of biological slight positive charge (δ+) on the hydrogen macromolecules and their composition. atoms. Water is a simple molecule composed of two smalls, positively charged hydrogen atoms Biochemical processes give rise to the and one large negatively charged oxygen atom. complexity of life; When the hydrogens bind to the oxygen, it creates an asymmetrical molecule with a positive charge 1. Lipids on one side and a negative charge on the other 2. Nucleic Acids side (Figure 2). This charge differential is called 3. Carbohydrates polarity and dictates how water interacts with 4. Proteins other molecules. Figure 2. Water Molecules. A. Water is held together by Hydrogen Bonds Hydrogen bond- formed by the electrical attraction between one H atom approaches the O of a second water molecule. Figure 1. Biomolecules and their properties. - Molecules carrying charges (ions) likewise (Level 1: Monomers units, level 2: macromolecules, level 3: interact favorably with water. Such molecules are supramolecular complexes and level 4: The cell and its termed hydrophilic. Hydrophobic molecules, are organelles) uncharged and form few or no hydrogen bonds, Chemical Components of a Cell and so do not dissolve in water. Living organisms are made of only a small B. Water as a universal Solvent selection of the 92 naturally occurring elements, As a polar molecule, water interacts best with four of which—carbon (C), hydrogen (H), other polar molecules. The bonding makes water nitrogen (N), and oxygen (O)—make up 96.5% of molecules stick together in a property called an organism’s weight. cohesion. The cohesion of water molecules helps plants The atoms of these elements are linked take up water at their roots. Cohesion also together by covalent bonds to form molecules. contributes to water’s high boiling point, which Because covalent bonds are typically 100 times helps animals regulate body temperature (Figure stronger than the thermal energies within a cell, Water also helps cells transport and use they resist being pulled apart by thermal motions, substances like oxygen or nutrients. and they are normally broken only during specific chemical reactions with other atoms and molecules. Two different molecules can be held together by noncovalent bonds, which are much weaker. Figure 3. Properties of water Cohesion and Adhesion. Cohesion- water molecules are attracted to one another through hydrogen bonds. Adhesion- water molecules are attracted to the xylem walls through hydrogen bonds. These properties of water are important for the movement of water but are not enough to move water up a tree. Figure 4. The four main families of small organic molecules in cells. C. Water the Aqueous Environment An aqueous solution is a solution in which By weight, macromolecules are the most water is a solvent. Aqueous from the word abundant carbon-containing molecules in a living aqua means pertaining or dissolved in water. cell. The macromolecules in cells are polymers The aqueous solution is water with a pH of 7.0, that are constructed by covalently linking small where the 𝐻+and 𝑂𝐻−are in Arrhenius organic molecules (called monomers) into long chains. balance 10−7. A non-aqueous solution is a solution in which the solvent is not water. Nonelectrolytes are substances that dissolve in water yet maintain their molecular integrity e.g. sugar, urea, glycerol, and methylsulfonylmethane (MSM). Cell is formed from Carbon Compounds Carbon is outstanding among all the elements in its ability to form large molecules. Carbon is small and has four electrons and four vacancies in its outermost shell, a carbon atom can form four covalent bonds with other atoms. Figure 5. Cells are composed of water, inorganic ions, The carbon compounds made by cells are called and carbon-containing (organic) molecules. Water is the organic molecules. In contrast, all other most abundant molecule in cells, accounting for 70% or molecules, including water, are said to be more of total cell mass. inorganic. Certain combinations of atoms, such as the The inorganic ions of the cell, including sodium (Na+), potassium (K+), magnesium (Mg2+), methyl (–CH3), hydroxyl (–OH), carboxyl(– calcium (Ca2+), phosphate (HPO42-), chloride (Cl-), and COOH), carbonyl (–C=O), phosphate (–PO32− ), bicarbonate (HCO3-), constitute 1% or less of the cell sulfhydryl (–SH), and amino (–NH2) groups, occur mass. These ions are involved in a number of aspects repeatedly in the molecules made by cells. of cell metabolism, and thus play critical roles in cell function. Molecular Composition of the Cell Cells Contain Four Major Families of Small Furthermore, cells contain most of organic Organic Molecules compounds belong to one of four classes of molecules: These small molecules form the monomeric carbohydrates, lipids, proteins, and nucleic acids. building blocks, or subunits, for most of the Proteins, nucleic acids, and most carbohydrates (the macromolecules and other assemblies of the cell. polysaccharides) are macromolecules formed by the Some, such as the sugars and the fatty acids, are also joining (polymerization) of hundreds or thousands of energy sources. low-molecular-weight precursors: amino acids, nucleotides, and simple sugars, respectively. Such macromolecules constitute 80 to 90% of the dry weight of most cells.  Carbohydrates. Simple sugars, such as glucose, respectively. Oleate is an unsaturated 18-carbon fatty acid are the major nutrients of cells. The basic formula containing a double bond between carbons 9 and 10. Note for these molecules is (CH2O)n, from which the that the double bond introduces a kink in the hydrocarbon chain. name carbohydrate is derived (C= “carbo” and H2O= “hydrate”). The six-carbon (n= 6) sugar glucose (C6H12O6) is especially important in cells, Nucleic Acids. The nucleic acids—DNA and since it provides the principal source of cellular RNA—are the principal informational molecules energy. of the cell. DNA and RNA are polymers of nucleotides, which consist of purine and pyrimidine bases linked to phosphorylated sugars. A nucleic acid base linked to a sugar alone is a nucleoside. Nucleotides additionally contain one or more phosphate groups (Figure 8). Figure 6. Representative sugars containing three, five, and six carbons (triose, pentose, and hexose sugars, respectively) are illustrated. Sugars with five or more carbons can cyclize to form rings, which exist in two alternative forms (α and β) depending on the configuration of carbon 1. Lipids. The simplest lipids are fatty acids, which consist of long hydrocarbon chains, most frequently containing 16 or 18 carbon atoms, with a carboxyl group (COO-) at one end. Unsaturated Figure 8. Components of nucleic acids. fatty acids contain one or more double bonds between carbon atoms; in saturated fatty acids all of the carbon atoms are bonded to the maximum number of hydrogen atoms. Figure 9. Structure of amino acids Each amino acid consists of a central carbon atom (the α carbon) bonded to a hydrogen atom, a carboxyl group, an amino group, and a specific side chain (designated R). At physiological pH, both the carboxyl and amino groups are ionized. Proteins. Proteins are polymers of 20 different amino acids. It is considered the most diverse of all macromolecules, and each cell contains several thousand different proteins, which perform a wide variety of functions. The roles of proteins include serving as structural components of cells and Figure 7. Structures of Fatty acids tissues, acting in the transport and storage of small Fatty acids consist of long hydrocarbon chains terminating in a carboxyl group (COO-). Palmitate and stearate are molecules (e.g., the transport of oxygen by saturated fatty acids consisting of 16 and 18 carbons, hemoglobin), transmitting information between cells (e.g., protein hormones), and providing a  defense against infection (e.g., antibodies). The How Cells Obtain Energy from Food most fundamental property of proteins, however, Glycolysis is a Central ATP-Producing Pathway is their ability to act as enzymes. - major process for oxidizing sugars in the sequence of reactions. It came from the Greek word glukus, Catalysis and the Use of Energy by Cells “sweet,” and lusis, “rupture”. Enzymes, a specialized class of proteins, help - produces ATP without the involvement of molecular control chemistry in living cells by binding to oxygen. substrates and reducing activation energy for specific - occurs in the cytosol of most cells, including many chemical reactions. A catalyst is a substance that anaerobic microorganisms. lowers the activation energy of a reaction, increasing the rate of chemical reactions by allowing more What is the process of glycolysis? random collisions with surrounding molecules to kick During glycolysis, a glucose molecule with six the substrates over the energy barrier. carbon atoms is converted into two molecules of pyruvate, each of which contains three carbon atoms. For each glucose molecule, two molecules of ATP are hydrolyzed to provide energy to drive the early steps, but four molecules of ATP are produced in the later steps. At the end of glycolysis, there is consequently a net gain of two molecules of ATP for each glucose molecule broken down. Two molecules of the activated carrier NADH are also produced. Fermentations Produce ATP in the absence of Oxygen. For most animal and plant cells, glycolysis is only a prelude to the final stage of the breakdown of food molecules. In these cells, the pyruvate formed by How Enzymes Find Their Substrates: The glycolysis is rapidly transported into the Enormous Rapidity of Molecular Motions mitochondria, where it is converted into CO2 plus An enzyme will often catalyze the reaction of acetyl CoA, whose acetyl group is then completely thousands of substrate molecules every second. This oxidized to CO2 and H2O. means that it must be able to bind a new substrate Fermentations are energy-producing molecule in a fraction of a millisecond. But both processes which frequently involve anaerobic enzymes and their substrates are present in relatively conditions and organic compounds that can both small numbers in a cell. How do they find each other contribute and take electrons. The assembly of the so fast? whole glycolytic pathway in the 1930s saw an Rapid binding is possible because the motions important milestone for biochemistry, which followed caused by heat energy are enormously fast at the quickly by the discovery of ATP's crucial function in molecular level. These molecular motions can be cellular operations. classified broadly into three kinds: 1. The movement of a molecule from one place to The Citric Acid Cycle another (translational motion), - The citric acid cycle takes place inside mitochondria 2. The rapid back-and-forth movement of in eukaryotic cells. covalently linked atoms with respect to one - The citric acid molecule is then gradually oxidized, another (vibrations), and; allowing the energy of this oxidation to be harnessed 3. Rotations to produce energy-rich activated carrier molecules. The rates of molecular motions can be - In addition to pyruvate and fatty acids, some amino measured by a variety of spectroscopic techniques. A acids pass from the cytosol into mitochondria. large globular protein is constantly tumbling, rotating - Both the citric acid cycle and glycolysis also function about its axis about a million times per second. as starting points for important biosynthetic reactions Molecules are also in constant translational motion, by producing vital carbon-containing intermediates, which causes them to explore the space inside the cell such as oxaloacetate and α-ketoglutarate. very efficiently by wandering through it—a process - Most chemical energy is released in the last stage in called diffusion. As the molecules in a liquid collide and the degradation of a food molecule. bounce off one another, an individual molecule moves - At the end of this series of electron transfers, the first one way and then another, its path constituting a electrons are passed to molecules of oxygen gas (O2) random walk. that have diffused into the mitochondrion, which simultaneously combine with protons (H+) from the 2. Kreb's cycle. surrounding solution to produce water. The remaining two carbons from the pyruvate feed - The electrons have now reached a low energy level, into a complicated set of reactions called the Kreb's and all the available energy has been extracted from cycle. The Kreb's cycle produces 8 more NADH the oxidized food molecule. This process, termed molecules and two molecules of FADH2. Again, both of oxidative phosphorylation. these are carrying energy rich electrons. 3. Electron transport phosphorylation Types of cellular respiration Most of the NADH and FADH2 travel to special There are two basic types of cellular respiration membranes in the cell which have a series of aerobic cellular respiration and anaerobic cellular molecules called the electron transport system that respiration. Aerobic respiration requires the use of harvest the energy rich electrons from the NADH and oxygen and anaerobic respiration which does not use FADH2 and use that energy to male lots of ATP by a oxygen. There are several types of anaerobic process called electron transport phosphorylation. If respiration, most familiar is a process called we are dealing with aerobic respiration this is where fermentation. the oxygen becomes important. Aerobic Respiration. Aerobic respiration is the process by which ATP is produced by cells by the complete oxidation of organic compounds using oxygen. In aerobic respiration oxygen serves as the final electron acceptor, accepting electrons that ultimately come from the energy rich organic compounds we consume. We will use glucose as an illustration of an organic molecule used in cellular respiration since glucose is a common energy source for cells. Stages in Aerobic Respiration: Aerobic Respiration takes place in three stages 1. Glycolysis Glycolysis is the first step in cellular respiration and all cells regardless of the type of cellular respiration they do are able to carry out glycolysis. Because of this we believe that glycolysis probably arose very early in the evolution of life on the planet. In glycolysis glucose is partially oxidized and broken down into two 3 carbon molecules called pyruvate or II. PROTIENS pyruvic acid. In the process, glycolysis produced 4 ATP for a net gain of two ATP and two molecules of NADH. Proteins are large and complex Each NADH is carrying two energy rich electrons away macromolecules that are vital to living organisms. from the glucose and these electrons can be used by It is also called the “Building blocks of life” which the cell to do work. came from the Greek word “proteios” which After glycolysis the pyruvate is processed to means “of first importance”. It was coined by harvest 2 more NADH molecules and remove one Jöns Jacob Berzelius in 1838. carbon per pyruvate. The carbon and two oxygens is Proteins are composed of amino acids removed since it no longer has any useful energy. So it (monomer) bonded together by peptide bonding is waste. This little step is the source of some of the to form a polypeptide chain (polymer). They are carbon dioxide we produce. bonded through dehydration synthesis (Figure 10). Note that glycolysis itself is anaerobic, in that oxygen is not required.  Figure 10. Protein Structure The Central Dogma of Molecular Biology Figure 11. Primary protein structure Protein Transcription- transcribed genetic code from the mRNA will be translated into a CHAIN OF B. Secondary protein structure. the repetitive AMINO ACIDS folding of polypeptide chains by hydrogen mRNA is read as three sets of nucleotides called bonds between the hydroxyl (OH) group and CODONS the hydrogen molecule of the adjacent amino Transfer RNA (tRNA) will then carry the specific acid, leading to the unique shape of the amino acids into the complementary codons of protein. (e.g. Alpha helix and Beta-pleated the mRNA. sheet) The amino Acids will then form PEPTIDE BONDS to and become a POLYPEPTIDE CHAIN OF AMINO Alpha-helix ACIDS -The polypeptide chains twisted into a right- handed screw a coil made consisting of Protein Translation- when a specific protein hydrogen bonding between several amino needs to be produced, a segment of the DNA that acids' carbonyl groups and amino groups. codes for that protein is transcribed into a - outstanding tensile strength due to its molecule called messenger RNA (mRNA). stability and strong bonding. Protein folding- where the polypeptide chain Beta-pleated sheet adopts into its supposed three-dimensional shape - The polypeptide chains are stretch out to function properly. beside one another and bonded by intermolecular H-bonds. PROTEIN STRUCTURE - In this structure, all peptide chains are A. Primary protein structure. It contains the stretched out to nearly maximum extension exact ordering of amino acids forming their and then laid side by side which is held chains. Simplest level of the protein structure. together by intermolecular hydrogen bonds - one dimensional, and the only interaction - parallel or antiparallel present is the peptide bonding. Primary protein structure is when amino acids bound are together via covalent peptide bonds to form a polypeptide chain. These bonds form between the N terminal and C terminal of amino acids and are highly resistant to heat or chemicals. Figure 12. Secondary protein structure C. Tertiary protein structure. Polypeptide D. Quaternary protein structure. when multiple chain folding into a distinctive 3D structure polypeptide chains link together to form a functioning -This tends to be globular in shape and unit. contains a binding site for the protein action. -produced and stabilized by the same kinds of Folding of the polypeptide chain occurs via interactions that produce and maintain the an interaction between the R groups of amino tertiary structure acids. - the most complex level of organization that is - If the links between R groups are broken, the still regarded as a single molecule. tertiary structure can become disordered, - protein must have two or more peptide chains losing its shape and its ability to perform its acting as subunits in order to be categorized as job this process is called protein having quaternary structure. denaturation. - protein is generally referred to as a dimer, trimer, or tetramer depending on how many TYPE OF BONDS IN TERTIARY STRUCTURE subunits it contains. 1. Hydrostatic bonds – form between the hydroxyl (OH) group and an adjacent Table 1. Fibrous vs Globular Proteins. hydrogen molecule, providing a strong bond between polar R groups. FIBROUS GLOBULAR Long and narrow Round/ spherical 2. Electrostatic bonds – form between structural Functional positive and negative charge. They can be stable structure Unstable structure disrupted by the presence of other Repetitive amino acid Irregular amino acid charged molecules near them. sequence Less sensitive to More sensitive to 3. Covalent disulphide bonds – form changes in pH, changes in pH, between sulphide groups within the R temperature, etc. temperature, etc. group of amino acids. They usually occur e.g. Keratin, myosin, e.g. enzyme, insulin, between two cysteine amino acids, which fibrin, actin elastin immunoglobulin and contain sulphur within their R groups. and collagen hemoglobin Insoluble in water Soluble in water 4. Hydrophobic bonds – form between non- polar groups and commonly involve the benzene group. 3. LIPIDS Lipids have three major roles in cells. First, they provide an important form of energy storage. Second, and of great importance in cell biology, lipids are the major components of cell membranes. Third, lipids play important roles in cell signaling, both as steroid hormones (e.g., estrogen and testosterone) and as messenger molecules that convey signals from cell surface receptors to targets within the cell It came from the Greek "lipos" which referred to animal fat or vegetable oil. It was introduced in 1923 by the French pharmacologist Gabriel Bertrand. Properties of lipids -They are organic compounds formed of fats and oils. Lipids produce high energy and perform Figure 13. Types of bonds in tertiary structure. different functions within a living organism, such 1.Simple Lipids: Simple lipids are triglycerides, as: esters of fatty acids, and wax esters. The Lipids stored in kidney. hydrolysis of these lipids gives glycerol and fatty Lipids are generally hydrophobic, meaning acids. they repel water and do not dissolve in it. Lipids are formed from hydrocarbon chains, 2.Complex Lipids: Complex or compound lipids and they are heterogeneous in nature. are the esters of fatty acids with groups along Fats and oils, in the form of triglycerides, are with alcohol and fatty acids. Examples are efficient energy storage molecules, providing Phospholipids and Glycolipids. a concentrated source of energy when broken down. 3.Derived lipids: Derived lipids are the Phospholipids are essential components of hydrolyzed compounds of simple and complex cell membranes, forming the lipid bilayer that lipids. Examples are fatty acids, steroids, fatty defines cellular boundaries. They help in the aldehydes, ketone bodies, lipid-soluble vitamins, selective permeability of a cell membrane. and hormones. Lipids like cholesterol and steroid hormones consists of four-ring structure and function in membrane fluidity and cellular signaling. Lipids provide essential fatty acids that the body cannot produce on its own and allow the absorption of fat-soluble. CLASSIFICATIONS OF LIPIDS Lipids are classified based on their chemical reactivity and the nature of their constituent molecules into two groups as follows: 1. Nonsaponifable Lipids- cannot be hydrolyzed or saponified using alkaline hydrolysis. (e.g. cholesterol (a steroid) and carotenoids) 2. Saponifiable Lipids- can be hydrolyzed or saponified using alkaline hydrolysis. (e.g. Triglycerides). It is further divided into; Polar Lipids: also known as amphipathic Figure 14. Classifications of lipids lipids because they have both hydrophilic (water-attracting) and hydrophobic (water- Phospholipids are amphipathic. Lipid repellent) regions within their molecular structure is typically made of a glycerol backbone, structure. Examples of polar lipids include 2 fatty acid tails (hydrophobic), and a phosphate phospholipids and glycolipids. group (hydrophilic) (Figure 15). Non- Polar Lipids: are hydrophobic and do not have a significant hydrophilic component in their structure. They are primarily involved in energy storage and insulation. For example, Triglycerides (fats and oils). Lipids are mainly classified into three types. They are simple, complex, and derived lipids. Figure 15. Phospholipid. 4. CARBOHYDRATES It came from the French term 'hydrate de carbone', which simply means 'hydrate of carbon'.It is also called saccharides which is derived from a Greek word called 'Sakkharon’ that means sugar. It is considered the most common type of organic compound such as sugar or starch, and is used to store energy built of small, repeating units that form bonds with each other Figure 16. Monosaccharide. to make a larger molecule. It contains only carbon, hydrogen, and oxygen. 2. Disaccharides -Two monosaccharides combine to form a disaccharide. made up of two monosaccharides bonded together by a glycosidic (covalent) bond. The following are some of the common disaccharides: - Sucrose-glucose + fructose (e.g., table sugar) - Lactose-glucose + galactose (milk sugar) - Maltose-α-D-Glucose + β-D-Glucose (malt sugar) Figure 16. Classification of Carbohydrates The carbohydrates are further classified into simple and complex which is mainly based on their chemical structure and degree of Figure 17. Disaccharides. polymerization. 3. Oligosaccharides 1. Monosaccharides - It is made by bonding together three or more (3 -The simplest carbohydrates; most of them are to 15) monosaccharides bonded together. sugars such as mannose, galactose, fructose or - Raffinose (glucose + fructose + galactose; 3 glucose. Glucose is the form of carbohydrates sugars) found in circulating blood (blood sugar) and is the - Stachyose (glucose + fructose + 2 galactose; 4 primary carbohydrate used by the body for sugars) energy production. - oligosaccharides are commonly found in beans - Fructose, or “fruit sugar,” is found in ripened and legumes. fruits and honey and is also formed by digestion - Some oligosaccharides are used as substances to of disaccharide sucrose. enhance the growth of good microbes - Galactose is found along with disaccharide (prebiotics). lactose in mammalian milk and is released during digestion. - They are classified based on numbers of carbons in a sugar. Triose (3 C) Tetrose (4 C) Pentose (5 C; e.g., Xylose and Ribose) Hexose (6 C; e.g., glucose, fructose, galactose, and mannose)  Figure 20. Amylopectin-α 1,4 linkage with alpha 1,6 linkage at branch. Figure 18. Oligosaccharide. Table 1. Amylose vs Amylopectin 4. Polysaccharides AMYLOSE AMYLOPECTIN - Polysaccharides are complex carbohydrates A straight-chain A branched-chain formed by the polymerization of a large number polymer of D-glucose polymer of D-glucose of monomers. units units - most important carbohydrate in animal feed. Constitute 20% of Constitute 80% of - It composed of many single monosaccharide starch starch units linked together in long, complex chains. Soluble in water Insoluble in water - It includes energy storage in plant cells (e.g., Straight chain Branched structure seed starch in cereal grains) and animal cells (e.g., structure glycogen) or structural support (plant fiber). B. Glycogen Homopolysaccharide form of starch found in animal tissue and is -Contains only one type of saccharide unit. hence called animal starch. -Examples of homopolysaccharides that are a polysaccharide that is physically related to important in animal nutrition include starch amylopectin with basic alpha-D-Glucose but has a (nonstructural form), glycogen (animal form), mix of α 1,4 and α 1,6 bonds. Glycogen exists in a and cellulose (plant structural form). small amount (< 1%) in liver and muscle tissue. A. Starch: Principal sugar form of carbohydrate C. Cellulose in cereal grains (seed energy storage). The the most abundant carbohydrate in nature. It basic unit is α-D-Glucose. Forms of starch in provides structural integrity to plant cell walls. cereal grains include Cellulose is highly stable. No animal enzyme can break it; only microbial cellulase can degrade it. Ruminant animals such as cattle, however, have bacteria in their rumen that contain the enzyme cellulase. Heteropolysacharride -a component of plant cell walls with a mix of 5 C Figure 19. Amylose-α 1,4 linkage-straight chain, and 6 C sugars nonbranching, helical structure - hemicellulose and pectin, a mixture of pentose and hexose units. Amylose is the simplest of the polysaccharides, being comprised solely of glucose units joined in an alpha 1,4 linkage. III. CELL SURFACE OF THE EXTRACELLULAR Facilitated diffusion- diffusion of specific MATRIX particles through membrane transport proteins to help them move through the cell Cell Membrane- surrounds the cytoplasm of membrane. living cells, physically separating the intracellular components from the extracellular environment. Two types of membrane transport proteins involved: A. Channel proteins- contain tunnels/ openings that serve as passageways of molecules. B. Carrier proteins- undergo temporary binding to molecule it carries resulting in conformational change that moves the molecule through the membrane. Figure 23. Protein channel proteins. Figure 21. Cell Transport Mechanism. also called permeases, are usually quite specific, and they only recognize and transport a limited variety of chemical Passive process: substances. Some substances (small molecules, ions) such as carbon dioxide (CO) and oxygen (O), can move Active process: across the plasma membrane by diffusion, which -Cells uses energy (ATP) is a passive transport process. -Moment from an area of low concentration to an The rate of diffusion is affected by the size of area of high concentration (LOW-HIGH) the molecules (the smaller the faster) and temperature (the warmer the faster). Osmosis- the presence of different solutes in the water solutions in and out of the cell means contrition of water on both sides is different. Water potential- movement of water molecules as it undergoes osmosis. Figure 22. Osmosis. Diffusion of water through a selectively permeable membrane  vesicle which will carry the molecules inside the cytoplasm (figure 25). Figure 25. Types of endocytotic transport. B. Exocytosis: Forces material out of the cell in bulk by invagination and formation of a vesicle (figure 26). -membrane surrounding the material fuses with cell membrane -cell changes shape which requires energy Figure 24. Na-K pump Types of Bulk Transport A. Endocytosis- the process in which cells absorb molecules by engulfing. - Use energy - Cell membrane in-folds around the macromolecule to be transported - 3 TYPES OF ENDOCYTOCIS Figure 26. Exocytosis. 1. PHAGOCYTOCIS- (cell eating) process by which cells take in large particles by infoldings the cell membrane to form CELL ADHESION- A process where binding with other endocytotic vesicle (figure 25). cells or with the extracellular matrix (ECM) occurs. 2. PINOCYTOSIS- (cell drinking) process of taking in fluids into the cell by invagination CELL ADHESION MOLECULES (CAMS)- It is the of cell membrane. Any solute or small subset of cell adhesion proteins located on the cell particles in the fluid will move into the cell surface involved in binding with other cells or with the (figure 25). extracellular matrix. -It helps cells stick to each other and to their 3. RECEPTOR-MEDIATED ENCOCYTOSIS- surroundings. (cell drinking) compared to pinocytosis, is - It plays an integral role in creating force and very specific. The plasma membrane movement and consequently ensure that organs are becomes indented and forms a pit. The pit able to execute their functions. lined with the receptor proteins picks -Important in affecting cellular mechanisms of growth, specific molecules from its surroundings. contact, inhibition, and apoptosis. The pit will close and pinch off to form a  VACUOLE FORMATION -are fluid-filled, enclosed structures that are separated from the cytoplasm by a single membrane. FUNCTIONS OF PLANT VACUOLE Turgor Pressure Control Growth of the central vacuole aids in cell elongation Storage vacuoles store important minerals, water, nutrients, ions, waste - products, small molecules, enzymes, and plant pigments. Molecule degradation It composed of three conserved domains: Detoxification 1.An intracellular domain that interacts with the Protection cytoskeleton, Seed Germination 2. A transmembrane domain, and 3. An extracellular domain. TYPES OF BONDING: Homophilic binding- CAMs bind to same CAMs Heterophilic binding- CAMs bind to different CAMs The final type of binding occurs between cells and substrate, where a mutual extracellular ligand binds two different CAMs. Figure 28. Autolysis SIGNAL TRANSDUCTION-the process of transferring Autolysis- a programmed cell death in plants a signal throughout an organism, especially across or naturally occurring process where the plant’s own through a cell. It relies on proteins known as receptors, enzymes destroy it. The vacuole ruptures releasing its which wait for a chemical, physical, or electrical signal. contents in the cytoplasm. The digestive enzyme released from the vacuole degrades the entire cell (Figure 28). EXTRACELLUAR MATRIX The word extracellular means “outside the cell.” This space is found outside the plasma membrane, and is occupied by fluids. Structures found in the extracellular fluid play roles such as maintenance if cell structure, cell adhesion, migration, division, differentiation and apoptosis. It is also called cellular soup It plays a role in buffering the effects of the environment and allow as barrier to separate tissues, making it appear more physically distinct. Applications of the cellular matrix include growth support (e.g. bone growth) and wound healing. Figure 27. Three stages of signal transduction 1. Reception, 2. Transduction and Response Chemical signals are called ligands, and can be produced by organisms to control their body or received from the environment. Receptor proteins are specialized by the type of cell they are attached to. It acquires specific coordinated response as it receives signals. COMPONENTS OF THE EXTRACELLULAR MATRIX Glycosaminoglycans (GAGs), which is a group found Mostly made up of water, fibrous proteins, and in the proteoglycan, allows it to resist against the proteoglycans compression. Made up of relatively sturdy fibrous proteins: collagens, elastin, and laminins. GLYCOSAMINOGLYCAN (GAGS) The sturdiness of these proteins helps the ECM Chains of sugar that varies maintain its environment and resist force, Highly negatively charged molecule produced by allowing it to withstand environmental pressures animal cells without collapsing EXTRACELLULAR FLUID FUNCTIONS OF ECM: - is known as interstitial fluid, and surrounds most of Filler that lies between cells in a tissue the cells in the body. Water retention and homoestatic balance Provide major support for each organ and tissue. Blood plasma- Extracellular fluid that travels in the circulatory system and is the liquid component of ECM is composed of two main classes of blood. macromolecules ; 1. Proteoglycans Interstitial fluid- Allows cells to carry out processes 2. Fibrous protein using the nutrients and oxygen provided, and to carry wastes back to the blood. There are four main fibrous proteins that make up the ECM; Transcellular Fluid 1. COLLAGEN It is the final fluid which meant to provide structural Main structural component of the ECM, as well as support most multicellular animals Can be found in the eye, joint, and cerebrospinal fluid Most abundant fibrous protein Made from fibroblasts Makes up roughly ⅓ of total protein mass in animals. Stretch resistance and tensile strength (i.e. scar formation during wound healing) 2. ELASTIN Fiber that lends tissues ability to recoil and stretch without breaking Stretch and resilience 3. FIBRONECTINE Regulates division and specialization in many tissue types. Secreted by fibroblast cells in water-soluble form, but quickly changes once assembles in a undissolvable mesh Cell migration and positioning within the ECM, and cell division and specialization in various tissues. CELL SIGNALING- is a general term referring to the many and varied processes by which 4. LAMININ communications controlling cell-level activities Good at assembling itself into sheet-like protein are generated, maintained, used, and networks that acts as a glue that connects dissimilar terminated. tissue types - Cells communicate with non-adjacent cells by Present at the junctions where connective tissue - releasing signaling elements into the nearby meet muscle, nerve, or epithelial lining tissue. cellular environment or into the blood. - Cell Signaling Pathways can be categorized based PROTEOGLYCANS on the distance over which the signaling occurs. Resists against compression TYPES OF CELL SIGNALING 2. Enzyme-coupled receptors- are Juxtacrine signaling - (also known as direct cell transmembrane proteins which as of 2009, only signaling) is the process by which cells that are in six types were known. They are; direct contact with one another communicate with Receptor tyrosine kinases each other. Tyrosine kinase associated receptors Paracrine signaling - occurs between cells which are Receptor-like tyrosine phosphatases close together, sometime directly, sometimes via Receptor serine/ threonine kinases extracellular fluid. Receptor Guanylyl cyclase’s Endocrine signaling - involves signaling over large Histidine kinase associated receptors distances, often where the signaling molecule is transported in the circulatory system. 3. G-protein-coupled receptors – are the largest Auto signaling - cell stimulates a response within of all the cell surface receptors. Due to the large itself by releasing signals for its own receptor. variety of cellular processes that GPCR's are involved in, they are usually an attractive target Hormones are often used as cell signaling for the development of drugs to treat a variety of molecules and sometimes will caused to response disorders. environmental changes. These receptors mediate responses involving hormones, local mediators and neurotransmitters. MAJOR RECEPTORS OF MEMBRANE PROTEINS 1. G-PROTEIN-COUPLES RECEPTORS Receptors are protein molecules in the target cell or 2. ION CHANNEL RECEPTORS on its surface that bind ligands. There are two types of 3. ENZYME-LINKED RECEPTORS receptors: internal receptors and cell-surface receptors. HOW CELLS RESPOND TO SIGNALS? TYPES OF RECEPTORS Once a receptor protein receives a signal, it ▪ Internal receptors, also known as intracellular or undergoes a conformational change, which in turn cytoplasmic receptors, are found in the cytoplasm of launches a series of biochemical reactions within the the cell and respond to hydrophobic ligand molecules cell. that are able to travel across the plasma membrane. These intracellular signaling pathways, also called ▪ Cell-surface receptors, also known as trans- signal transduction cascades, typically amplify the membrane receptors, are cell surface, membrane- message, producing multiple intracellular signals for anchored, or integral proteins that bind to external every one receptor that is bound. ligand molecules. This type of receptor spans the Activation of receptors can trigger the synthesis of plasma membrane and performs signal transduction, small molecules called second messengers, which converting an extracellular signal into an intracellular initiate and coordinate intracellular signaling signal. pathways. 3 MAIN COMPONENTS OF CELL-SURFACE RECEPTORS FOR CELL SIGNALS RECEPTORS A cell surface receptor exists intrinsically embedded in 1. External ligand-binding domain (extracellular the plasma membrane. domain) 2. A hydrophobic membrane-spanning region It has two domains of significance - the signal 3. Intracellular domain inside the cell molecule binding domain, which is exposed to the exterior of the cell and the intra-cellular 3 GENERAL CATEGORIES OF CELL SURFACE domain in contact with the cytoplasm. RECEPTORS 1. Ion channel linked receptors- bind a ligand CELL SURFACE RECEPTORS 3 MAIN CLASSES and open a channel through the membrane that 1. Ligand-gated ion channel receptors-also allows specific ions to through. To form a of cell- known as ionotropic receptors, are responsible surface receptor has an extensive membrane- for the rapid transmission of signals across spanning region. synapses in the nervous system by allowing a 2. G-protein-linked receptors -bind a ligand and flow of ions across the plasma membrane, which activate a membrane protein called a G-protein. changes the membrane potential, causing an The activated G-protein then interacts with electrical current. either an ion channel an enzyme in the membrane.  3. Enzyme-linked receptors- are cell-surface receptors with intracellular domains that are associated with an enzyme. AGONIST VS ANTAGONIST ▪ An agonist is a ligand that binds to a receptor and produces a biological effect (direct acting) or a compound that indirectly produces the same effect of a neurotransmitter (indirect acting). ▪ An antagonist is a ligand that binds to a receptor but does not produce biological effect (direct acting) or a compound that indirectly inhibits the effect of a neurotransmitter (indirect acting). These compounds usually block or inhibit the actions of a neurotransmitter. ANTAGONIST Figure 29. Direct contact A competitive antagonist binds to the same site as the agonist but does not activate it, thus blocks the 2. PARACRINE SIGNALING. Signal molecules agonist’s action. released by cells can diffuse through the A non-competitive antagonist binds to an allosteric extracellular fluid to other cells. Signals with such (nonagonist) site on the receptor to prevent activation short-lived, local effects are called paracrine of the receptor. signals. Like direct contact, paracrine signaling A reversible antagonist binds non-covalently to the plays an important role in early development, receptor, therefore can be “washed out”. An coordinating the activities of clusters of irreversible antagonist binds covalently to the neighboring cells. receptor and cannot be displaced by either competing 3. ENDOCRINE SIGNALING. If a released signal ligands or washing molecule remains in the extracellular fluid, it may enter the organism’s circulatory system and travel NOTCH SIGNALING widely throughout the body. These longer-lived ▪ The Notch signaling pathway is a fundamental signal molecules, which may affect cells very signaling system used by neighboring cells to distant from the releasing cell, are called communicate with each other in order to assume their hormones, and this type of intercellular proper developmental role. Notch proteins are cell communication is known as endocrine signaling. surface transmembrane spanning receptors which mediate critically important cellular functions through direct cell-cell contact. ▪ The Notch pathway regulates cell proliferation, cell fate, differentiation, and cell death in all metazoans. TYPES OF CELL SIGNALING 1. DIRECT CONTACT. When cells are very close to one another, some of the molecules on the cells' plasma membranes may bind together in specific ways. Many of the important interactions between cells in early development occur by means of direct contact between cell surfaces.  processes, including metabolism and immune response. CELL SURFACE RECEPTORS CHEMICALLY GATED CHANNEL -When cells are very close to one another, some of the molecules on the cells' plasma membranes may bind Figure 30. Paracrine & Endocrine together in specific ways. Many of the important interactions between cells in early development occur 4. SYNAPTIC SIGNALING by means of direct contact between cell surfaces. - ln animals, the cells of the nervous system provide rapid communication with distant cells. ENZYMATIC RECEPTORS Their signal molecules, neurotransmitters, do not - Enzymic receptors are single-pass transmembrane travel to the distant cells through the circulatory proteins, with the part binding the signal molecule system like hormones do. Rather, the long, fiber outside the cell and the enzymatic part exposed to the like extensions of nerve cells release cell's interior. neurotransmitters from their tips very close to the G-PROTEIN LINKED RECEPTORS target cells. The narrow gap between the two cells - They indirectly influence enzymes or ion channels in is called a chemical synapse. While paracrine the cell membrane with the help of a protein called a G signals move through the fluid between cells, protein. It also assists in transmitting the signal from neurotransmitters cross the synapse and persist the cell membrane's surface to the interior of the cell. only briefly. INTERCELLULAR ADHESION RECEPTORS THAT ACT AS GENE REGULATORS Junction- Connections between cells within tissues. CORTISOL - is a steroid hormone produced by the - are not just casual touches but are long-lasting and adrenal glands in response to stress and various essential for maintaining the structure and functions physiological signals. of tissues in a multicellular organism. a) When cortisol is released into the bloodstream, it circulates throughout the body. b) Inside target cells, cortisol binds to specific intracellular receptors known as glucocorticoid receptors (GR). c) This binding activates the glucocorticoid receptor, and the hormone receptor complex then enters the cell nucleus. d) In the nucleus, the cortisol-activated receptor binds to specific DNA sequences, called glucocorticoid response elements (GREs), to regulate the transcription of genes involved in various cellular  Figure 31 Junctions. A. Gap junction, b. desmosome, c. tight junction Cell junctions are divided into three categories, based upon the functions they serve: tight junctions, anchoring junctions, and communicating junctions. TIGHT JUNCTIONS - Sometimes called occluding junctions, tight junctions connect the plasma membranes of adjacent cells in a sheet, preventing small molecules from leaking between the cells and through the sheet. ANCHORING JUNCTIONS - Anchoring junctions Figure 32. Types of anchoring junction. mechanically attach the cytoskeleton of a cell to the cytoskeletons of other cells or to the extracellular Gap Junctions - Communicating Junctions: Gap matrix. They are commonest in tissues subject to junctions are specialized structures found in animal mechanical stress, such as muscle and skin epithelium cells that serve as communicating junctions. They play (Figure 32). a vital role in allowing cells to communicate and share small molecules and ions with each other. COMMUNICATING JUNCTIONS - Communicating junctions establish direct physical connections Connexons: The key components of gap junctions that link the cytoplasm of two cells together, are structures called "connexons." Each connexon permitting small molecules or ions to pass from is made up of six identical transmembrane one to the other. In animals, these direct proteins. These proteins are arranged in a circular communication channels between cells are called pattern, creating a channel through the cell's gap junctions. In plants, they are called plasma membrane. plasmodesmata. Channel Formation: Connexons create channels that protrude several nanometers from the cell's surface. These channels serve as passageways between adjacent cells. Aligning Connexons: A functional gap junction is formed when the connexons of two neighboring cells align perfectly, creating an open channel that spans the plasma membranes of both cells. Passage of Small Substances: Gap junctions are selective in what they allow to pass through. They permit the passage of small substances like simple sugars and amino acids, which are important for cell communication and coordination. Size Selectivity: Gap junctions, however, prevent the passage of larger molecules such as proteins. This selectivity is essential for maintaining cellular  integrity and preventing the movement of Nuclear pore- A nuclear pore is a minute opening or potentially harmful substances between cells. passageway through the nuclear envelope. It connects Connexon Dynamics: Gap junction channels are the nucleoplasm (nucleus) with the cytoplasm. The dynamic structures that can open or close in opening is 'plugged' with an amazing biological valve response to various factors, including the that only permits selected chemicals to move into and presence of calcium ions (Ca²⁺) and hydrogen ions out of the nucleus. The word 'pore' is derived from the (H⁺). This ability to open and close is known as Greek 'poros' which translates to 'passage' "gating." Protective Function: Gap junctions serve a Nucleolus- The nucleolus is the largest structure in protective function as well. When a cell is the nucleus of eukaryotic cells. It is best known as the damaged, its plasma membrane may become site of ribosome biogenesis, which is the synthesis of leaky, allowing ions in high concentrations outside ribosomes. the cell, like calcium ions (Ca²⁺), to flow into the damaged cell. Nucleoplasm- the thick fluid inside the nucleus of a -When these ions enter the damaged cell, they can cell, where the DNA and other molecules are stored cause further harm. To prevent this, the gap junction and processed. channels between the damaged cell and its neighbors are shut down by the influx of calcium ions (Ca²⁺). This Chromatin- Chromatin is composed of histones and isolation prevents the damage from spreading to other DNA. A 147 bp of DNA chain wrapped around the 8- cells. core histone forms the basic chromatin unit, the nucleosome. Ribosomes- A ribosome is a complex cellular mechanism used to translate genetic code into chains of amino acids. Long chains of amino acids fold and IV. Nucleus function as proteins in cells. "Control center of the cell" Chromosome Serves both as the repository of genetic information -The substance consisting of all the chromosomes in a and as the cell's control center. cell and all their associated proteins is known as chromatin. -Each chromosome is made up of DNA tightly coiled many times around proteins called histones that support its structure. -Chromosome has a constriction point called the centromere; which divides the chromosome into two sections or arms: "p" - The short arm of the chromosome. "q" - The long arm of the chromosome Figure 33. Nucleus. 23 pairs and 46 chromosomes Nuclear envelope- a highly regulated membrane -1-22 chromosomes are AUTOSOMES meaning they barrier that separates the nucleus from the cytoplasm are not related to your biological sex. Their genes are in eukaryotic cells. It contains a large number of related to eye color, height, hair texture etc. different proteins that have been implicated in chromatin organization and gene regulation. -The 23rd chromosome either XX (female) chromosome or XY (male) chromosome, is the SEX -Note although the nuclear membrane enables CHROMOSOME and determines your biological sex. complex levels of gene expression, it also poses a challenge when it comes to cell division. Trivia: Chromosomes are not visible in the cell's nucleus, not even under a microscope when the cell is not dividing. Chromosome in Prokaryotes and Eukaryotes CHROMOSOME NUMBER A prokaryotic cell typically has only a single, HAPLOID: Contains 23 chromosomes or one complete coiled, circular chromosome. Located at the set (n). This is characteristic of germ cells. nucleoid. DIPLOID: most normal somatic cells contain 46 chromosomes or two complete sets (2n). CHROMOSOME MORPHOLOGY POLYPLOID: A few normal somatic cells contain three Chromosomes can be classified based on the position or more complete sets of chromosomes (Xn) and are of their centromere. therefore a polyploidy. A. METACENTRIC CHROMOSOME: Centromere ANEUPLOID: Cells that have an irregular number of is present in the middle and divides the chromosomes (45 or 47) are said to be aneuploidy. chromosome into two equal arms. B. SUB-METACENTRIC CHROMOSOME: Karyotyping Centromere is slightly away from the middle A karyotype is the general appearance of the region. In this, one arm is slightly longer than complete set of chromosomes in the cells of a species the other. or in an individual organism, mainly including their C. ACROCENTRIC CHROMOSOME: Centromere sizes, numbers, and shapes. Typical karyotype is done is located close to one of the terminal ends. In not during Anaphase and Telophase because in these this, one arm is extremely long and the other is stages, chromosomes are separated into single extremely short. chromatids. D. TELOCENTRIC CHROMOSOME: Centromere So, for optical viewing karyotype must be done is located at one of the terminal ends. at or right before the Metaphase. In arranging karyotypes chromosomes are arranged in homologous pairs. Homologous chromosomes are same in size, same type of genes, and in a homologous pair you receive one chromosome from the father and another one from the mother. Cell Cycle -a series of events that takes place in a cell as it grows and divides. Figure 34. Classification of chromosomes based on centromere. A cell spends most of its time in what is called interphase, and during this time it CHROMOSOME BANDING grows, replicates its chromosomes, and prepares for cell division. Q-BANDS: These bands are seen after staining with the fluorescent dye quinacrine. They are thought to MITOSIS & MEIOSIS represent chromatin regions particularly rich in adenine-thymine base pairs. G-BANDS: These bands are similar to the Q-bands but can be visualized in an ordinary light microscope. The staining procedure involves denaturation of chromosomal proteins followed by Giemsa stain. C-BANDS: These bands are very different from the Q- and G-bands. The staining procedure involves harsh treatment to extract DNA followed by Giemsa stain. Centromere region of each chromosome and distal portion of Y chromosome; highly repetitive, mostly AT-rich DNA.  Figure 35. MITOSIS & MEIOSIS Pyknosis- The nucleus is condensing or getting smaller because it shrinks. CELLULAR DIFFERENTIATION AND PROLIFERATION Karyorrhexis- The nucleus starts to rupture and turns to fragments. Cell proliferation- refers to the process which results in an increase of the number of cells. Karyolysis- The nucleus fragments break Cell differentiation- refers to the process by which down further into their basic blocks. Hence, it a less specialized cell becomes a more specialized cell dissolves away. type. CENTRAL DOGMA The central dogma illustrates the flow of genetic information in cells, DNA replication, and coding for the RNA through the transcription process, and further RNA codes for the proteins by translation. 1. DNA REPLICATION- The process begins with Figure 36. Nuclear indicator of cell death. DNA replication, where the organism's genetic material is duplicated. This process is essential to TRANSPORT ACROSS NUCLEAR ENVELOPE maintain genetic continuity in the newly formed cell during cell division. Depending on their size, molecules can travel through the nuclear pore in either direction: 2. RNA TRANSCRIPTION- After DNA replication the cytoplasm to nucleus or nucleus to cytoplasm. process continues to RNA transcription. In this process, DNA information is transcribed into mRNA, a Nuclear transport depends on signals for type of RNA molecule that contains the instructions or import or export. These signals are referred to recipe that directs the cells to make a protein using its as nuclear localization signals (NLSS) or natural machinery. nuclear export signals (NES). rRNA Processing- Ribosomal RNA (rRNA) processing NLSS or NESS are recognized and bound by is the series of steps that occur to create functional soluble import or export receptors that ribosomes in a cell. shuttle between nucleus and cytoplasm. 3. PROTEIN TRANSLATION- Protein translation is a process that occurs on ribosomes in the cell The interaction of the receptors with their cytoplasm, where mRNA is read and translated into cargoes (or substrates) can be direct or the string of amino acid chains that make up the mediated by an additional adapter protein. synthesized protein. Each group of three bases in mRNA constitutes a codon, and each codon specifies a Upon binding, the transport receptors dock particular amino acid (hence, it is a triplet code). The their cargoes to the nuclear pore and facilitate mRNA sequence is thus used as a template to their translocation across the central channel assemble—in order—the chain of amino acids that of the pore. form a protein. After delivering their cargoes, the receptors Nuclear Matrix are recycled to initiate additional rounds of The nuclear matrix means the filamentous transport. An export receptor (R) binds its web of chromatin (DNA + protein), substrate (S) in the nucleus and carries it organizing the DNA in a way that facilitates through the nuclear pore into the cytoplasm. transcription and replication. Nuclear Organization- refers to the spatial distribution of chromatin within a cell nucleus. Nuclear Indicators of Cell Death: Chromosome Territory Model- the DNA fiber of multiple chromosomes meanders through the nucleus in a largely random fashion, and the chromosomes are therefore intermingled and entangled with each other. “Spaghetti” Model- the DNA of each chromosome occupies a defined volume of the nucleus and only overlaps with its immediate neighbors. Gene Expression The process by which the instructions in our DNA are converted into a functional product such as protein and non-coding RNA such as phenotype. Gene Regulation- Regulation of gene expression includes a wide range of mechanisms that are used by cells to increase or decrease the production of specific gene products. How do cells decide which gene to turn on? Cell’s gene expression decision is determined by a process that happen within a cell when it receives a signal from outside. Signal transduction pathway. Over expression- Overexpression of genes occur when the amount of a particular protein produced by a gene is higher than normal. Under expression- Under expression of genes refer to the insufficient or abnormally low expression of certain genes, it occurs when the production of a particular protein by a gene is lower than normal.